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New hydrogel technology has promise in breast cancer modelling

In science, a model is used as a representation of something in the real world, so that ideas and concepts may be tested out. Models have a variety uses, but in cancer biology they are often popular as they can help to mimic the complex environment seen in human   disease. Models are used to explore the effects of new drugs, understand genetic or cellular pathways on tumour development or predict the potential response of a patients cancer.

It’s in a researcher’s best interest to create a model that is as faithful to the real world as possible, so that the outcomes are accurate and can translate successfully into humans. However, the go-to models to recapitulate human cells in a lab use, a protein matrix extracted from mouse tumours, which is used to resemble the extracellular environment found human tumours. But the extent to which mouse matrix can be used is limited by its fixed extracellular matrix components, which are often not representative of the human tissue, and the inability to add or remove the individual extracellular components to explore the influence these on tumour growth.

Dr Gillian Farnie, Nuffield Department of Orthopaedics, Rheumatology and Musculorskeletal Sciences, has focused her work on developing new models that allow human breast cancer cells to be grown and researched, whilst overcoming these limitations.

A recent publication in Matrix Biology, funded by the NC3Rs, outlines a new peptide hydrogel developed by the Farnie group in collaboration with Prof Merry (University of Nottingham).  This new peptide hydrogel offers the added benefit of being customisable, by incorporating or removing specific extracellular matrix components that researchers want to test, to better understand their influence on cancer cells. It therefore allows full control over the biochemical and physical properties of the model, providing researchers with the opportunity to more accurately adapt the model to the real-life environment of human breast tumour.

The new technology’s applications are incredibly widespread and promising. For example, certain extracellular matrix proteins, when found in high quantities in a tumour, can often be associated with a poorer prognosis for a patient. Researchers may want to understand if this is a simple correlation, or if the proteins are assisting the cancer in some way, such as promoting treatment resistance. The ability to remove these proteins from a cancer model and test the response, whilst remaining faithful and accurate to human cells, is incredibly useful and can allow us to discover therapeutic targets.

Dr Gillian Farnie is currently working with the breast cancer research community to apply this new technology in multiple breast tumour research projects. The hydrogel’s applications are not limited to just matrix biology, but also in investigating areas such as the biological significance of blood vessel supply to tumours or even other cancer types outside the breast.

This new hydrogel provides an opportunity to better understand the individual influences of the extracellular matrix, mechanical properties and cell-cell interactions on breast cancer and other disease. It is an open and reproducible model that Dr Farnie is currently publishing a detailed methodology in JOVE, so that more cancer researchers can have access to the new technology.

About this research

Dr Gillian Farnie is based in the Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences.  Her research focuses on the development of patient derived pre-clinical breast cancer models that are used to examine mechanisms of inherent and induced therapy resistance, interrogating both intra-tumour heterogeneity (cancer stem cells) and the tumour microenvironment (ECM, Stroma, Immune cells).

New AI technology to help research into cancer metastasis

Cell migration is the process of cells moving around the body, such as immune cells moving through the body’s tissues to fight off disease, or the cells that move to fill the gap where a tissue has been injured. Whilst cell migration is an important process for regeneration and growth, it is also the process that allows cancer cells to invade and spread across the body.

Therefore understanding the factors that regulate and instruct cells to move is an important part of understanding how we can prevent the metastasis of many cancers. One method of doing this is through scratch assays, which as the title suggests, involves inflicting a wound or ‘scratch’ on cells grown in a petri-dish and analysing how the surrounding cells react and migrate to ‘heal’ the scratch under a microscope.

Although cell migration is intensively studied, we still do not have efficient therapies to target it in the context of cancer metastasis. Observing cancer cell behaviour to artificial wounding and how this can be altered in response to pharmacological drug treatment or gene editing is important to fully understand the factors that drive this process in tumours and provide insights on the processes that drive such behaviours. Whilst current microscopic analysis methods of wound healing data are hindered by the limited image resolution in these assays. Therefore, there is a need to develop new methods that overcome current challenges and help to answer these questions.

Dr Heba Sailem a Research Fellow from the Department of Engineering, has led a study to develop a new deep learning technology known as DeepScratch. DeepScratch can detect cells from heterogenous image data with a limited resolution, allowing researchers to better characterise changes in tissue arrangement in response to wounding and how this affect cell migration.

Tests using the technology have found that DeepScratch can accurately detect cells in both membrane and nuclei images under different treatment conditions that affected cell shape or adhesion, with over 95% accuracy. This out-performs traditional analysis methods, and can also be used when the scratch assays in question are applied to genetically mutated cells or under the influence of pharmaceutical drugs – which makes this technology applicable to cancer cell research too.

Dr Heba Sailem says;

“Scratch assays are prevalent tool in biomedical studies, however only the wound area is typically measured in these assays. The change in wound area does not reflect the cellular mechanisms that are affected by genetic or pharmacological treatments.

“By analysing the patterns formed by single cells during healing process, we can learn much more on the biological mechanisms influenced by certain genetic or drug treatments than what we can learn from the change in wound area alone.”

Using this technology, the team have already observed that cells respond to wounds by changing their spatial organisation, whereby cells that are more distant from the wound have higher local cell density and are less spread out. Such reorganisation is affected differently when perturbing different cellular mechanisms. This approach can be useful for identifying more specific therapeutic targets and advance our understanding of mechanisms driving cancer invasion.

The team predicts that DeepScratch will prove useful in cancer research that studies changes in cell structures during migration and improve the understanding of various disease processes and engineering regenerative medicine therapies. You can read more about DeepScratch and its applications in a recent study published in Computational and Structural Biotechnology.

About Heba

Dr Heba Sailem is a Sir Henry Wellcome Research Fellow at the Big Data Institute and Institute of Biomedical Engineering at the University of Oxford. Her research is focused on developing intelligent systems that help further biological discoveries in the field of cancer.

New digital classification method using AI developed for colorectal cancer

A new study from S:CORT demonstrates an easy, cheap way to determine colorectal cancer molecular subtype using AI deep-learning digital pathology technology

New start-up Base Genomics launches

 

About the technology

TET-assisted pyridine borane sequencing (TAPS) is a new method for measuring DNA methylation, a chemical modification on cytosine bases. DNA methylation has important regulatory roles in the cell but is frequently altered in cancer. These altered DNA methylation levels are preserved in DNA that is released into the blood from cancer cells and therefore DNA methylation has great potential as the basis for a multi-cancer blood test. However, a key limitation to achieving this aim, especially for detecting cancer at the earliest stages, is the low sensitivity of current DNA methylation technology.

One of the advantages of TAPS over the current standard methodology is the avoidance of the use of bisulphite, a harsh chemical that severely degrades DNA. TAPS is a mild reaction that preserves DNA integrity and is effective at very low DNA concentrations, which would increase the sensitivity of blood-based DNA methylation assays. TAPS also better retains sequence complexity, enabling simultaneous collection of DNA methylation and genetic data, and cutting sequencing costs in half. Read more about the potential of TAPS as the basis for a multi-cancer blood test here.

The company Base Genomics has been launched to set a new gold standard in DNA methylation detection using this TAPS technology.

 

“I am thrilled about the launch of Base Genomics and look forward to seeing the TAPS technology developed in my lab applied to new technologies for cancer detection and the advancement of a variety of fields of biomedical research,”

Dr Chunxiao Song, assistant member of the Ludwig Institute Oxford Branch, co-founder of Base Genomics, chemistry advisor to the company.

 

 “Genomic technologies with the power, simplicity and broad applicability of TAPS come along very infrequently,

“It has the potential to have an impact on epigenetics similar to that which Illumina’s SBS chemistry had on Next Generation Sequencing.”

Base Genomics CTO Dr Vincent Smith.

 

About Base Genomics

Base Genomics has a team of leading scientists and clinicians, including Dr Vincent Smith, a world-leader in genomic product development and former Illumina VP; Professor Anna Schuh, Head of Molecular Diagnostics at the University of Oxford and Principal Investigator on over 30 clinical trials; Drs Chunxiao Song and Yibin Liu, co-inventors of TAPS at the Ludwig Institute for Cancer Research, Oxford; and Oliver Waterhouse, previously an Entrepreneur in Residence at Oxford Sciences Innovation and founding team member at Zinc VC.

The company has closed an oversubscribed seed funding round of $11 million USD (£9 million GBP), led by Oxford Sciences Innovation alongside investors with industry expertise in genomics and oncology. This funding will progress development of the TAPS technology, initially focusing on developing a blood test for early-stage cancer and minimal residual disease.

 

”The ability to sequence a large amount of high-quality epigenetic information from a simple blood test could unlock a new era of preventative medicine,

“In the future, individuals will not just be sequenced once to determine their largely static genetic code, but will be sequenced repeatedly over time to track dynamic epigenetic changes caused by age, lifestyle, and disease.”

Base Genomics founder and CEO Oliver Waterhouse.

 

“In order to realise the potential of liquid biopsies for clinically meaningful diagnosis and monitoring, sensitive detection and precise quantification of circulating tumour DNA is paramount,

“Current approaches are not fit for purpose to achieve this, but Base Genomics has developed a game-changing technology which has the potential to make the sensitivity of liquid biopsies a problem of the past.”

Base Genomics CMO Professor Anna Schuh

 

For more information, see the Base Genomics press release.

 

Oxford technology holds great promise for a multi-cancer blood test

Ongoing Oxford research aims to improve the sensitivity of cancer blood tests with the goal of earlier detection for a variety of cancers.

Focussed ultrasound and nanomedicine offer new hope for improving effects of cancer drugs

Researchers have made a breakthrough in more precisely targeting drugs to cancers.

A number of Centre members were part of a multi-disciplinary team of biomedical engineers, oncologists, radiologists and anaesthetists that have used ultrasound and lipid drug carriers (liposomes) to improve the targeting of cancer drugs to a tumour. The new technology has been used in humans for the very first time, with ultrasound remotely triggering and enhancing the delivery of a cancer drug to the tumour.

“Reaching therapeutic levels of cancer drugs within a tumour, while avoiding side effects for the rest of the body is a challenge for all cancer drugs, including small molecules, antibodies and viruses” says Professor Constantin Coussios, Director of the Oxford Centre for Drug Delivery Devices and of the Institute of Biomedical Engineering at the University of Oxford. “Our study is the first to trial this new technique in humans, and finds that it is possible to safely trigger and target the delivery of chemotherapy deep within the body from outside the body using focussed ultrasound. Once inside the tumour, the drug is released from the carrier, supplying a higher dose of chemotherapy directly to the tumour, which may help to treat tumours more effectively for the same or a lower systemic dose of the drug.”

The 10-patient phase 1 clinical trial, supported by the Oncology Clinical Trials Office, used focused ultrasound from outside the body to selectively heat liver tumours and trigger drug release from heat-sensitive carriers, known as thermosensitive liposomes. Building on over a decade of preclinical studies, the study demonstrated the ultrasound technique to be feasible, safe, and capable of increasing drug delivery to the tumour between two-fold and ten-fold in the majority of patients. Ongoing research worldwide is investigating the applicability of this technique to other tumour types, and future research could explore the combination of ultrasound with other drugs.

All 10 patients treated had inoperable primary or secondary tumours in the liver and had previously received chemotherapy. The procedure was carried out under general anaesthesia and patients received a single intravenous dose of 50 mg/m2 of doxorubicin encapsulated within low-temperature-sensitive liposomes (ThermoDox®, Celsion Corporation, USA). The target tumour was selectively heated to over 39.5° C using an approved ultrasound-guided focussed ultrasound device (JC200, Chongqing HAIFU, China) at the Churchill Hospital in Oxford. In six out of ten patients, the temperature at the target tumour was monitored using a temporarily implanted probe, whilst in the remaining four patients ultrasonic heating was carried out non-invasively.

Before ultrasound exposure, the amount of drug reaching the tumour passively was low and estimated to be below therapeutic levels. In seven out of 10 patients, chemotherapy concentrations within the liver tumour following focussed ultrasound were between two and ten times higher, with an average increase of 3.7 times across all patients.

“Only low levels of chemotherapy entered the tumour passively. The combined thermal and mechanical effects of ultrasound not only significantly enhanced the amount of doxorubicin that enters the tumour, but also greatly improved its distribution, enabling increased intercalation of the drug with the nucleus of cancer cells ” says Dr Paul Lyon, lead author of the study.

“This trial offers strong evidence of the rapidly evolving role of radiology in not only diagnosing disease but also guiding and monitoring therapy. The treatment was delivered under ultrasound guidance and patients were subsequently followed up by CT, MRI and PET-CT, evidencing local changes in tumours exposed to focussed ultrasound” commented Professor Fergus Gleeson, radiology lead co-investigator for the trial.

“A key finding of the trial is that the tumour response to the same drug was different in regions treated with ultrasound compared to those treated without, including in tumours that do not conventionally respond to doxorubicin” adds Professor Mark Middleton, principal investigator of the study. “The ability of ultrasound to increase the dose and distribution of drug within those regions raises the possibility of eliciting a response in several difficult-to-treat solid tumours in the liver. This opens the way not only to making more of current drugs, but also targeting new agents where they need to be most effective”.

The study was published in The Lancet Oncology journal.